Abstract
Early-maturity varieties of upland cotton are becoming increasingly important for farmers to improve their economic benefits through double cropping practices and mechanical harvesting production in China. However, fiber qualities of early-maturing varieties are relatively poor compared with those of middle- and late- maturing ones. Therefore, it is crucial for researchers to elucidate the genetic bases controlling fiber-quality related traits in early-maturity cultivars, and to improve synergistically cotton earliness and fiber quality. Here, multi-locus genome-wide association studies (ML-GWAS) were conducted in a panel consisting of 160 early-maturing cotton accessions. Each accession was genotyped by 72,792 high-quality single nucleotide polymorphisms (SNPs) using specific-locus amplified fragment sequencing (SLAF-seq) approach, and fiber quality-related traits under four environmental conditions were measured. Applying at least three ML-GWAS methods, a total of 70 significant quantitative trait nucleotides (QTNs) were identified to be associated with five objective traits, including fiber length (FL), fiber strength (FS), fiber micronaire (FM), fiber uniformity (FU) and fiber elongation (FE). Among these QTNs, D11_21619830, A05_28352019 and D03_34920546 were found to be significantly associated with FL, FS, and FM, respectively, across at least two environments. Among 96 genes located in the three target genomic regions (A05: 27.95 28.75, D03: 34.52 35.32, and D11: 21.22 22.02 Mbp), six genes (Gh_A05G2325, Gh_A05G2329, Gh_A05G2334, Gh_D11G1853, Gh_D11G1876, and Gh_D11G1879) were detected to be highly expressed in fibers relative to other eight tissues by transcriptome sequencing method in 12 cotton tissues. Together, multiple favorable QTN alleles and six candidate key genes were characterized to regulate fiber development in early-maturity cotton. This will lay a solid foundation for breeding novel cotton varieties with earliness and excellent fiber-quality in the future.
Highlights
Upland cotton (Gossypium hirsutum L.), a tetraploid plant, is the most important natural-fiber crop
To gain insight into the genetic bases of fiber-quality related traits, 160 early-maturity upland cotton accessions were performed using SLAF-seq, and a complete set of markers containing 72,792 high-quality single nucleotide polymorphisms (SNPs) was explored by filtering according to the stringent quality control
The SNP loci with maximal number were identified on chromosome
Summary
Upland cotton (Gossypium hirsutum L.), a tetraploid plant, is the most important natural-fiber crop. It is widely cultivated in the world and supplies more than 95% of the global fiber yield due to its extensive adaptive ability and high productivity (Chen et al, 2007). Early-maturity (short-season) cotton is an ecological type with a relatively short growing period (Yu et al, 2005; Song et al, 2015). The early-maturity upland cotton varieties are becoming more and more important in Chinese cotton production
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